This paper re-evaluates the economic organization of native populations living in Southern Chile through the Ceramic and Early Historical periods (400–1850 ce), by redressing the imbalance between the carpological and the anthracological record in archaeobotanical research. Through both lines of evidence, we present a new synthesis about how the past populations who inhabited a southern temperate forest environment through the Late Holocene utilized plant resources. We present new archaeobotanical data from the archaeological site of Los Catalanes cave, which exhibits a long-term sequence through the studied periods. Cultivation practices incorporated both foreign and locally domesticated plants, including Zea mays, Chenopodium quinoa and Phaseolus vulgaris from the Early Ceramic Period, chili (Capsicum sp.) from the later Ceramic period, and wheat (Triticum aestivum) from the Historic Period. However, substantial quantities of wild foods, fruits and nuts from woodland plants as well as herbaceous seed plants are found, while many more taxa represented in wood charcoal have a range of potential additional uses beyond fuel. Woodland taxa indicate an open mosaic, suggesting human shaping of woodlands from at least the Early Ceramic Period. We propose that during the Ceramic Period populations from Southern Chile practiced intermediate economies combining foraging and farming until as late as the start of the last millennium (~ 1000 ce), and that these economies managed a mosaic of human shaped woodlands.